How to enforce the used DATA input of a LUT?

Interesting. Is this research into PUFs in an FPGA, or creating a product that needs it? Just curious.

I think an .rcf is the only way to go. Back-annotate down to the routing level. Either assignments -> Back-Annotate, but if routing isn't available do "quartus_cdb --back-annotate=routing <project_name>". For more info, run "quartus_sh --qhelp".

This will back-annotate every location to the .qsf and every route to an .rcf. You're going to have to manually rip out what you don't want, and then with the .rcf modify it to use the input you want. Note that there is some wildcarding in .rcfs which might help.